You can migrate the application configuration using the export_site script provided with the Deployment Template. Got the the control folder of you application and runexport_site.bat file_path\..\file_name.xml

Then copy the file to your QA environment and run the following 4 commands:
~ import the siteimport_site.bat file_path\..\file_name.xml
~ run the baseline (you might have to copy data first and set flags)baseline_update.bat
~ push updated templates set_templates.bat
~ promote content promote_content.bat

Also look at the other get & set scripts in the control folder. There are lot of scripts to migrate individual component.